Happens so that there is no necessity to show in the menu point by default, and there is also a necessity to clean this point of the menu. But in Joomla necessarily there should be a menu point by default that will get rid of display of this, it is necessary in a file modules/mod_mainmenu/helper.php in the cycle beginning

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while (count ($rows) &&! is_null ($row = array_shift ($rows)))($rows) && !is_null($row = array_shift($rows)))
{
...
}

To add

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if ($row-> id == 1) continue;->id == 1) continue;

In this case 1 it ItemId point of the menu which is necessary for hiding.
UPD:
That in Joomla 1.7 to hide main it is necessary after

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{
  unset ($items [$i]);[$i]);
  continue;
}

To add

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if ($item-> id == 1) {->id == 1){
  unset ($items [$i]);[$i]);
  continue;
}